Trajectory SP808

Force field: martini_v2.2
Simulation length (ns): 5000
Electric field (kJ mol-1 nm-1 e-1): 0
Temperature (K): 300 (v-rescale)
Pressure (bar): 1 (Parrinello-rahman semiisotropic)
Number of particles: 19191
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P194 AP03942
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
PFLLSLIPSAISALKKL
Total charge (e): +2
Number of residues: 17
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 1.38
Longitudinal (e nm): 1.09
Transversal (e nm): 0.85
Hydrophobic Dipolar Moment (nm): 5.39
Longitudinal (nm): 5.11
Transversal (nm): 1.73
Secondary structure: Helix
Activity:

Download Files
  ITP file.
  JSON file.
  PDB file.

Click on any component to highlight it from the plot.
Upper leaflet
Lower leaflet

Lipids


Membrane model for: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
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Contacts per residue
(normalized by number of beads in the residue)
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Molecular Dynamics based descriptors
Average and standard deviation, calculated using the autocorrelation function (for time series) or the width of the distribution, for the last microsecond of the trajectory

Area per lipid
Membrane (nm2): 0.644091000 ± 0.000955462
Upper leaflet (nm2): 0.644091000 ± 0.000955462
Lower leaflet (nm2): 0.644091000 ± 0.000955462
Average Z coordinate
Peptide (nm): 5.256440 ± 0.034263
First Residue (nm): 5.2066500 ± 0.0455391
Last Residue (nm): 5.0837600 ± 0.0473526
Membrane (nm): 6.82150000 ± 0.00945693
Upper leaflet Head Group (nm): 8.779860 ± 0.011373
Lower leaflet Head Group (nm): 4.85908000 ± 0.00771202
Bilayer Thickness (nm): 3.9207800 ± 0.0137412
Peptide insertion (nm): -0.3973650 ± 0.0351202
Contacts
Peptide - Water: 18.825000 ± 0.574775
Peptide - Head groups: 10.970000 ± 0.211947
Peptide - Tail groups: 12.040000 ± 0.287798
Tilt (°): 82.88800 ± 1.42962
PepDF:
5(ns):  CVS
Displacement (nm): 0.722447 ± 0.028931
Precession(°): -2.49265 ± 1.93535
50(ns)  CVS
Displacement (nm): 2.295810 ± 0.120763
Precession(°): -25.3123 ± 4.5756
100(ns)  CVS
Displacement(nm): 2.871410 ± 0.154908
Precession(°): -53.7737 ± 6.1089
200(ns)  CVS
Displacement(nm): 4.065730 ± 0.178454
Precession(°): -105.42100 ± 8.19654

  Download JSON File.

Peptide Analyses

Peptide Displacement Fingerprint (PepDF)
Lateral displacement vs Rotational Displacement along the trajectory, for different time windows .

Density maps:
2D-density maps of lipids around the peptide along XY and YZ axis, calculated for each lipid type along the last microsecond.

Lipid-Peptide Analyses:

z-Position
Z-coordinate, averaged for differetn parts of the the system: peptide, membrane, first and last backbone (BB) residues and upper of lower leaflet lipids’ headgroups (HGs).
Minimum distance
Minimum distance (nm) between the peptide backbone and the lipids (headgroups and tailgroups).
Number of contacts
Number of contacts between the peptide backbone and the water or the lipids separated by lipid headgroups (HG) or lipid tails, using a cut-off of 0.6 nm.
Lateral density
Lateral density for the different components of the system: headgroups, tail groups, peptide and water.